Bowel Disease, Part IV: Restoring Healthful Gut Flora

A healthy gut is a multi-species society: it is the cooperative product of the human body with trillions of bacterial cells from a thousand or more species.

An unhealthy gut is, more often than not, the product of a breakdown in this collaboration. Often, it is triggered by displacement of cooperative, commensal species of bacteria by pathogenic bacteria, fungi, viruses, and protozoa. This is why a long course of antibiotics, killing commensal bacteria, is often the prelude to bowel ailments.

It is difficult for the immune system to defeat gut infections without the help of commensal bacteria. Think about what the immune system has to deal with. The ulcers in ulcerative colitis are essentially the equivalent of infected skin abscesses, but in the colon. Here is a description of a bowel lesion in Crohn’s disease:

Ileal lesions in Crohn’s disease (CD) patients are colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells. [1]

Now imagine an infected skin abscess, but with feces spread over it three times a day, or stomach acid and digestive enzymes. How quickly would you expect it to heal?

Commensal “probiotic” bacteria are like a mercenary army fighting on behalf of the digestive tract. By occupying the interior lining of the digestive tract, they deprive pathogens of a “home base” that is sheltered from immune attack. If commensal bacteria dominate the gut, the immune system can usually quickly defeat infections.

This suggests that introduction of probiotic bacteria to the gut should be therapeutic for bowel disease.

Probiotic Supplements Are Inadequate

Most supermarket probiotics contain Lactobacillus or Bifidobacterium species. These species are specialized for digesting milk; they populate the guts of infants as they start breastfeeding, and are used by the dairy industry to ferment cheeses and yogurt.

These supplements are very effective at fighting acute diarrhea from most food-borne infections. A fistful of probiotic capsules taken every hour will usually quickly supplant the pathogens and end diarrhea.

However, against more severe bowel diseases caused by chronic infections and featuring damaged intestinal mucosa, these species are usually not helpful. One issue is that they provide only a tiny part of a healthful adult microbiome. A recent study surveyed the bacterial species in the human gut, and found these species to be most abundant [2]:

Figure: Abundant gut bacterial species

As this figure shows, Bacteroides spp. are the most common commensal bacteria, with Bacteroides uniformis alone providing almost 10% of all bacterial genes in the gut. Lactobacillus and Bifidobacterium do not appear among the 57 most abundant species.

This study showed, by the way, that patients with irritable bowel syndrome have 25% fewer types of bacterial gene in their gut than healthy people, and that the composition of bacterial genes in feces clearly distinguishes ulcerative colitis, Crohn’s disease, and healthy patients. In other words, in the bowel diseases a few pathogenic species have colonized the gut and entirely denuded it of about 25% of the commensal species that normally populate the gut. This finding supports the idea that restoring those missing species might be therapeutic for IBS.

Bacterial Replacement Therapies Work

So if IBS patients are missing 25% of the thousand or so species that should populate the gut, or 250 species, and if common probiotics provide only 8 or so species and not the ones that are missing, how are the missing species to be restored?

The answer is simple but icky. Recall that half the dry weight of stool consists of bacteria. A healthy person daily provides a sample of billions of bacteria from every one of the thousand species in his gut. They are in his stool.

So a “fecal transplant” of a healthy person’s stool into the gut of another person will replenish the missing species.

Scientists have known for a long time that this was likely to be an effective therapy, but it is only now entering clinical practice. The New York Times recently made a stir by telling this story:

In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took on a patient suffering from a vicious gut infection of Clostridium difficile. She was crippled by constant diarrhea, which had left her in a wheelchair wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but nothing could stop the bacteria. His patient was wasting away, losing 60 pounds over the course of eight months. “She was just dwindling down the drain, and she probably would have died,” Dr. Khoruts said.

Dr. Khoruts decided his patient needed a transplant. But he didn’t give her a piece of someone else’s intestines, or a stomach, or any other organ. Instead, he gave her some of her husband’s bacteria.

Dr. Khoruts mixed a small sample of her husband’s stool with saline solution and delivered it into her colon. Writing in the Journal of Clinical Gastroenterology last month, Dr. Khoruts and his colleagues reported that her diarrhea vanished in a day. Her Clostridium difficile infection disappeared as well and has not returned since.

The procedure — known as bacteriotherapy or fecal transplantation — had been carried out a few times over the past few decades. But Dr. Khoruts and his colleagues were able to do something previous doctors could not: they took a genetic survey of the bacteria in her intestines before and after the transplant.

Before the transplant, they found, her gut flora was in a desperate state. “The normal bacteria just didn’t exist in her,” said Dr. Khoruts. “She was colonized by all sorts of misfits.”

Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.” [3]

Fecal transplants can be done without a doctor’s help: someone else’s stool can be swallowed or inserted in the rectum. If taking feces orally, swallow a great deal of water afterward to help wash the bacteria through the stomach and its acid barrier.

Dogs and young children sometimes swallow feces. It is unpleasant to consider, but desperate diseases call for desperate measures. Perhaps one day, healthy stools will be available in pleasant-tasting capsules, and sold on supermarket shelves. Not yet.

Attacking Pathogenic Biofilms

Most bacterial species will build fortresses for themselves, called biofilms. These are polysaccharide and protein meshworks that, like bone, become mineralized with calcium and other minerals. These mineralized meshworks are built on bodily surfaces, like the gut lining, and protect bacteria from the immune system, antibiotics, and other bacterial species.

Biofilms favor the species that constructed them. So, once pathogens have constructed biofilms, it is hard for commensal species to displace them.

Therapies that dissolve pathogenic biofilms can improve the likelihood of success of probiotic and fecal transplant therapies. Strategies include enzyme supplements, chelation therapies, and avoidance of biofilm-promoting minerals like calcium. Specifically:

Polysaccharide and protease digesting enzymes. Human digestive enzymes generally do not digest biofilm polysaccharides, but bacterial enzymes that can are available as supplements. Potentially helpful enzymes include hemicellulase, cellulase, glucoamylase, chitosanase, and beta-glucanase. Non-human protease enzymes, such as nattokinase and papain, might also help. [5]

Chelation therapy. Since biofilms collect metals, compounds that “chelate” or bind metals will tend to gather in biofilms. Some chelators – notably EDTA – are toxic to bacteria. So EDTA supplementation tends to poison the biofilm, driving bacteria out of their fortress-shelter. This prevents them from maintaining it and makes the biofilm more vulnerable to digestion by enzymes and commensal bacteria. It also tends to reduce the population of pathogenic bacteria.

Mineral avoidance. The supply of minerals, especially calcium, iron, and magnesium, can be a rate-limiting factor in biofilm formation. Removal of calcium can cause destruction of biofilms. [6] We recommend limiting calcium intake while bowel disease is being fought, since the body can meet its own calcium needs for an extended period by pulling from the reservoir in bone. Upon recovery, bone calcium can be replenished with supplements. Iron is another mineral which promotes biofilms and might be beneficially restricted. We do not recommend restricting magnesium.

Some commercial products are available which can help implement these strategies. For instance, Klaire Labs’ InterFase (http://www.klaire.com/images/InterFase_Update_Article.pdf) is a popular enzyme supplement which helps digest biofilms, and a version containing EDTA is available (InterFase Plus).

Attacking Biofilms With Berries, Herbs, Spices, Vinegar, and Whey

Plants manufacture a rich array of anti-microbial compounds for defense against bacteria.

There is reason to believe that traditional herbs and spices, which entered the human diet during the Paleolithic and have been passed down through the generations for tens of thousands of years, were selected by our hunter-gatherer ancestors as much for their ability to promote gut health as for their taste. Dr. Art Ayers notes that:

Plants are adept at producing a wide array of chemicals with refined abilities to block bacterial functions. So when researchers sought chemicals to solve the problem of pathogens forming biofilms, it was natural to test plant extracts for inhibiting compounds. In a recent article [7], D.A. Vattem et al. added extracts from dietary berries, herbs and spices to bacterial pathogens, including the toxin producing Escherichia coli (EC) O157:H7, and checked for the ability to produce a chemical that signals the formation of a biofilm. The effective phytochemicals inhibited the bacteria from recognizing a critical density of bacteria, i.e. quorum sensing, and responding with the production of the biofilm-triggering chemical.

Blueberry, raspberry, cranberry, blackberry and strawberry extracts were effective as quorum sensing inhibitors (QSIs). Common herbs such as oregano, basil, rosemary and thyme were also effective. Turmeric, ginger and kale were also tested and found to contain QSIs. [8]

A few other remedies can weaken biofilms:

Acetic acid in vinegar can solubilize the calcium, iron, and magnesium in biofilms, removing these minerals and weakening the biofilm; citric acid binds calcium and can disrupt biofilms. [9]

Conclusion

Fecal transplants are the best probiotic. Tactics to disrupt pathogenic biofilms can assist probiotics in bringing about re-colonization of the digestive tract by commensal bacteria.

Along with a non-toxic diet (discussed in Part II) and nutritional support for the immune system and gut (discussed in Part III), these steps to improve gut flora make up a natural program for recovery from bowel disease.

UPDATE: Please read the cautions by two health professionals, annie and Jesse, about potential dangers of self-treatment with fecal transplants and EDTA. It is always better to pursue these therapies with a doctor’s assistance and monitoring.

380 Comments.

Hello,
I was wondering if you might be able to provide some advice. I have been struggling with a long list of related symptoms that seem to share the common root of inflammation. Specifically, I have rosacea, puffiness in my cheeks, post-nasal drip, frequent headaches, severe constipation (IBS), hypothyroidism, extremely low cholesterol, and a variety of neuropsychiatric symptoms (depression, anxiety, insomnia, and cognitive and motor problems). All of these symptoms have gotten progressively worse since taking several courses of antibiotics and then contracting an intestinal Campylobacter infection in 2009.
Some questions, if you don’t mind:

1. Is it possible that the acute phase of the Campylobacter infection has evolved into a chronic infection of some kind? Or is it likely that the severe diarrhea I experienced simply flushed my bowels of all healthy flora? My understanding of these issues is extremely vague. I have many symptoms of uncontrolled systemic inflammation, but it’s very difficult to precisely determine the source of the inflammation.

2. I have written to several gastroenterologists who are interested in exploring fecal bacteriotherapy, but all of them claim they are unwilling to perform this procedure on anyone without Clostridium difficile, citing the “need to be conservative.” Do you know of anyone in America or abroad who might be willing to consider this treatment for a patient with my list of symptoms? ( I am pretty firmly convinced that the majority of my symptoms would resolve with an effective restoration of healthy gut flora, but I’m not sure how best to accomplish this. Probiotic supplements in enormous doses have been nearly useless, and fermented foods (especially sauerkraut) tend to exacerbate all of my inflammatory symptoms–any idea why?)

3. Finally, I have done a significant amount of research on the relationship between SIBO (small bowel bacterial overgrowth) and rosacea specifically. My research indicates that there is a high likelihood that SIBO is a problem for me. Most of the information that I’ve found regarding SIBO indicates that (a) it’s usually diagnosed via hydrogen breath testing, and (b) it is normally treated with antibiotics, especially rifaximin. Given the profound impact of antibiotics on healthy gut flora, would you recommend treating SIBO with antibiotics? If so, would a fecal transplant be a viable method of restoring healthy flora after SIBO is cleared?

Thank you so much for your quick response! I would agree with your assessment as to why the fecal transplant may not work for Crohn’s. I’m hoping since I have Crohn’s colitis, it will work well for me. I will keep you posted.

I’m still waiting to get your book, just waiting for my Amazon gift card to arrive so I can purchase it :), so I only know what I’ve read here on your blog. As far as calcium, I understand you don’t recommend supplemental calcium, but should I limit dairy in general because of the calcium? Any suggestions as how much is too much dietary calcium, or should I only be concerned about it in my vitamins?

Thanks for the tips on the stool analysis. I’m hoping the doctor will order it for me, as I’d be very interested to see how it compares.

I think calcium from food is OK, including dairy. I think 500-600 mg/day is a reasonable level, but I don’t think a specific number is crucial as long as vitamin D levels are good.

Hi Brendan,

You have a complex case and I sympathize with your plight. On the one hand you need doctors to diagnose and treat your condition – it is beyond my ability to figure out just from symptoms, many things can cause those symptoms and you may have several problems at once – but our doctors are terrified of doing anything that’s not “standard practice” and might expose them to judgment. Of course “standard practice” will neither diagnose nor cure these conditions, which require a systematic exploratory approach.

I think the right thing to do is to start with better diagnosis. I would recommend the same test I suggested to Crohn’s girl, a fecal profile of pathogen DNA. Another good thing for you to look at a talk by Dr Ritchie Shoemaker who is a good example of the type of doctor you need to find. Check out his site survivingmold.com and look in the Diagnosis section. You can see one of his talks here: http://www.hcam.tv/videos/specials-and-unique-programs, go to the right side and scroll down till you see Hopkinton Drug Series – Dr Ritchie Shoemaker. He does a lot of diagnostic testing of innate immune markers, cell cultures from deep nasal scrapings, that sort of thing. I’m not saying his approach is the optimal one for you, but it is an example of the kind of systematic diagnostic approach that is needed to find the causes of your problems and enable effective choice of therapy.

Another thing he says is often helpful is cholestyramine, which binds bile and causes it to be excreted. This helps clear fat-soluble toxins, which most pathogens produce. Chlorella/chlorophyll and charcoal supplements do the same. Many people get some relief from this.

2. I don’t know of doctors. Fermented foods may increase symptoms when you have leaky gut as they introduce new species that can enter the body. Often a new species, or increased numbers of an existing one, trigger an immune response.

3. I’m not so convinced that SIBO is a cause of rosacea. I think rosacea is usually due to infections of the vasculature in the face that are derived from infections of the skin of the oral cavity. Often the same pathogens that infect the mouth infect the small intestine, since you’re constantly swallowing them. (Acid reflux can bring them the other way too.)

Thank you so much for your speedy reply. Incidentally, I have recently scheduled a case review with Chris Kresser, whose blog originally led me to your website. Do you think he might be able to help me sort out these issues?

Also, a couple of follow-up questions if you have the time:
1. If the campylobacteriosis did indeed lead to a chronic infection, would it be systemic or limited to the GI tract? Would the stool test you recommend be able to detect it?
2. If rosacea is caused by the same kinds of bacteria that infect the small bowel, wouldn’t clearing the small bowel of bacterial overgrowth and/or correcting overall gut flora imbalances be expected to improve rosacea?

Thanks again–you are so kind to respond to these questions in detail.
Best wishes,
Brendan

Hi,
Great series! I look forward to getting your book. I have Crohn’s and have been trying to heal naturally through diet and supplements and get off my meds(6MP). I’ve recently started taking a bovine colostrum supplement after reading anecdotal evidence that it has helped some people with IBD. I’ve read that it helps heal leaky gut and helps good bacteria adhere to the intestinal lining. However I’ve also read that it has IGF-1 which has been correlated with cancer. Since starting it, my abdominal pains have decreased greatly and I’ve been feeling much better. It has allowed me to reduce my 6MP dose. I don’t plan on taking the colostrum for very long, maybe 2-3 months at most. Have you done any research on colostrum? If so, what are your thoughts?

I think it’s great for IBD. Pathogen colonization of the intestine is possibly the greatest health threat to newborns, so milk has evolved a large number of molecules for shaping the gut flora in a positive direction. Of course, human colostrum would be ideal, but bovine colostrum performs a similar antimicrobial function with only mild risk of harmful effects.

IGF-1 is correlated with cancer and will make cancers progress faster, but the effect is modest. For instance, a low-protein diet decreases IGF-1 substantially and extends time to death 15-30% in animals with cancer. Taking bovine colostrum is probably a smaller increment of IGF-1 and might make an established cancer progress 5% faster. If you knew you had cancer this might affect your decision, but if you don’t know you have cancer and do know you have IBD, I would go with it as long as it is helping.

My doctor friend referred it to me after I gave her your book for a read. She read the book with an open mind even though many of the ideas were contrary to her views on nutrition.

After reading the book she attended a conference where a gastroenterologist discussed the dangers of gluten, fecal transplants, and the above study. She was surprised to find evidence confirming many of your views so quickly and in one place!

I’m going to do a series on rosacea as soon as my other responsibilities ease up.

Rosacea is a heterogeneous disease and the same therapies don’t work for everyone. I believe it is always infectious, but the nature of the pathogen can vary.

I believe that oral infections are important, and that generally the oral microbiota is the same as the small intestinal microbiota, since they are similar immune-mucosal environments and pathogens move between them in saliva (and acid reflux). I think rosacea involves a spread of the oral microbes to the vasculature of the face, or a vascular co-infection that is synergistic with oral pathogens. But inflammatory cytokines and lipopolysaccharides or other toxins generated in the gut are also important in causing inflammation and redness in the face.

Co-infectious rosacea may be common: the pathogen in the vasculature doesn’t need to be the same as the one in the mouth-bowel. Hydrogen and other gases generated in the bowel can circulate in the blood and feed the vascular infection. Inflammation generated in the mouth, or cytokines generated anywhere, can divert the immune system from healing a vascular infection.

The SIBO-rosacea connection has been around for a long time and though rifaximin sometimes works, many rosaceans have tried rifaximin without success. In the study less than half the rosaceans had SIBO, and presumably for the other half it wouldn’t have worked. Among the ones with SIBO, the numbers are better than I would have expected – especially the claim that the improvements were maintained for 9 months. Surprising there weren’t a number of regressions. Without changes in diet and oral hygiene, I wouldn’t expect antibiotic treatment success to be maintained.

In my case my rosacea seems to be due to Candida. Antibiotics never worked at all, but antifungals work well. Antifungal oral hygiene made a big difference for me.

Personally I have some facial redness and inflammation, as well as a tendency to mildly sore throats and mild sinus infections. I am curious whether these are all related and whether there are some steps I can take to determine whether it is fungal or bacterial and whether working on oral hygiene will help. What are the oral anti-fungal treatments that worked for you?

There are anti-fungal mouthwashes but I just used a homemade toothpaste of turmeric and white vinegar. (Turmeric and milk should work too.) Worked fine. Then I took a Blis K12 oral probiotic for bacteria.

Unfortunately the medical tests for fungal infections are almost non-existent. They can do a deep nasal scraping and culture it.

I have many health issues that began directly after antibiotic therapy. I am considering fecal tranplant and am wondering if I should first clear up my confirmed case of high levels of lead and mercury first before the implant or after.

Have you personally tried this procedure? Any thoughts on what measures to take to ensure a successful implant?

If you don’t mind sharing your advice again, which I greatly appreciate, after I get my fecal transplant done, do you suggest I stay away from natural antibiotic sources? I am currently taking bee propolis and manuka honey, both of which are supposed to have natural antibiotic and antifungal properties. Do you suspect that those would negatively affect the new beneficial bacteria from the transplant? Should I wait a certain time to add those back in?

Also, I ordered the Klairelabs Interphase enzymes to help break down the biofilms. Do you know any reason why I wouldn’t/shouldn’t be able to take that while I’m currently on antibiotics? Should I continue taking them after the transplant? Also, I saw that you eat a lot of cranberries to help break down biofilms, any suggestions on where you find fresh cranberries throughout the year?

I ordered your book last week and am anxiously awaiting it’s arrival. Thanks for hosting such a great blog and being a helpful resource for all of us. 🙂

Oh, one more thing- I clicked the “notify me of follow-up comments via email”, but I never get notified. Am I doing something wrong?

Interphase is mainly helpful for small bowel infections, whereas the fecal transplant mainly helps the colon. So they’re somewhat distinct. I would be cautious about EDTA which is in Interphase Plus. Some doctors recommend it but it can easily cause trouble.

I don’t think the cranberries need to be fresh; frozen will work too. I eat fresh cranberries in season when they’re available in our local markets. Other berries will also work; bilberries are supposed to be especially good.

I’m working on fixing the comment reply notification – hopefully I fixed it yesterday, but I need to test it. If you are notified of this reply can you let me know?

So, do biofilms not form in the colon? I suppose I should have done more research before I placed my order. I had assumed they could also form in the colon, so I thought those could help break down any biofilm in the colon and then help the fecal transplant to take better.

I didn’t receive a notification reply, but I will continue checking back.

Biofilms do form in the colon. Maybe it will help, I don’t know. Anecdotally most people don’t seem to be helped by EDTA, and the cases I’ve heard of it helping were primarily small bowel infections. I’m not sure you want to do anything during the prep that might irritate the GI tract. I’d be cautious.

Thank you for mentioning me in your “Around the Web edition”. I was quite thrilled to see that.

I wanted to share with you my recent experience. My son who is autistic recently came down with a bad ear infection about two weeks ago. Our pediatrician gave us antibiotics (erythromycin) to rid the infection. It definitely helped with the infection but I also noticed that he regressed in terms of his ability to focus and say words. He also started simming again which I haven’t seen in several months. He is off the antibiotics now and is starting to focus again. Even his school sent us a note home last week saying that he was misbehaving and not his normal self. I began to wonder if the antibiotics disrupted his gut flora which indirectly caused a disruption in brain function. The gut, immune system and the brain seem to be intertwined in autistic kids.

I have been reading your bowel disease articles. Autistic kids also have a lot bowel disorders as well. My son has many food allergies and troubles with digesting foods. It is quite complicated. He is allergic to dairy, wheat, soy and eggs. He has been on a gluten and casein free diet for about 7 months. Along with sensory issues, it can be challenging to get him to eat nutritious foods. Ironically, I have taken a PHD approach to treating my son. I try to eliminate food toxins and improve his nutritional needs by foods and supplements. Given his allergies and sensory issues, I have relied on vitamin supplements to fill in his nutritional needs. He takes a children’s multivitamin, 400mg of VitC, 100 mg of Mg, and 20 mg of B6 daily. I also add in a teaspoon of cod liver oil a few times a week for essential fatty acids and Vitamin D(1000IU). He doesn’t like fish yet.

After this antibiotic experience, I am trying to go in a direction that would promote more healthy gut bacteria in him. I found this study in pubmed that showed significant differences in gut flora between autistic and healthy kids.http://www.ncbi.nlm.nih.gov/pubmed/16157555

I wonder if fecal transplants would help kids with autism? I am also thinking about adding n-acetylcysteine to his vitamin cocktail since it helps with restoring glutathione and you mentioned it prevents biofilm formation. Any thoughts on whether probiotic supplements would be helpful? I found yogurt and kefir made from coconut that he likes and it contains a few species of bacteria. Or should I stick with probiotic rich foods?

Thanks for sharing your son’s experience, I will keep that in mind and think about what it might mean.

One thing I have learned from personal experience is that any time you have either chronic infections or a leaky gut, you get a lot of pathogen die-off toxins in the body. It can make a big difference to use things like charcoal, bentonite clay, chlorella, or cholestyramine to help excrete fat soluble toxins like bacterial lipopolysaccharide or fungal cell wall components. I’ve added these to our Supplement Recommendations page.

The paper you linked indicated it’s the toxins from gut Clostridium that may cause problems in autism.

In most cases it’s the immune activity that creates the biggest negative symptoms, so clearing toxins can substantially reduce symptoms. It also helps the immune system focus on the pathogens.

Probiotics I have found helpful include Lactobacillus reuteri and Primal Defense (not Ultra). If you suspect fungal infections then Bacillus subtilis will help. Then I think fermented vegetables are also valuable. We’ll do a Sunday recipe for home-made kimchi shortly.

Bone broth plus vegetable broth soups might be a good way to get some extra nutrition in him in a palatable way.

A fecal transplant is certainly a therapy to consider. Clostridium in the gut often flourishes after antibiotics, were high in autistic kids, and fecal transplants are most proven as a therapy for Clostridium. There the challenge would be finding a doctor willing to do it.

Thank you for your helpful suggestions and I plan to explore some of your ideas. There are some papers that have shown that a lot of kids with autism tend to have candida problems. Sometimes anti-fungals can be very helpful. I plan to get a profile of his gut flora and see if he has yeast as well. He hasn’t had a normal firm bowel movement in many months which makes me concerned. There was a short period where he had normal stools after wheat was removed from his diet. However, it didn’t last long. There are so many variables to consider.

Unfortunately, you are correct as many MDs are not helpful when it comes to trying alternative therapies such as a fecal transplants. They deffinitely take a hands off approach when it comes to treating autism. It can be very frustrating to a parent who is trying to find answers.

Checking in here and with another question hopefully you can answer. I had my fecal transplant done via colonoscopy last Friday and yesterday and today did some at home fecal enemas, since the protocols I’ve read for inflammatory bowel diseases had one via colonoscopy or nasal tube and then followed up with 4-9 more infusions via enema.

My donor doesn’t live close to me, so I was wondering if I could use the stool left over from today for the next two days, or do you think the beneficial bacteria would have already died?

I’ve read conflicting views on how long, most say within 6 hours to use, but the doctor that did the transplant on me said you could use it from the day before. Do you have any thoughts on this?

I think some species last better than others, so the mix of species will change. You don’t want to wait too long because pathogenic species tend to do better in oxygen and may be able to multiply in the stool, while commensal species like the oxygen-free environment of the colon.

I think your doctor’s idea of 24-36 hours is probably about right. I would trust your doctor’s experience.

Thanks for that information, Paul. I wasn’t aware of the oxygen issue.

So far so good, I’m cautiously optimistic. So far I’ve noticed a reduction in symptoms, so I hope that trend continues. I’ll keep you posted.

I’m hoping this therapy becomes more widely available via open-minded doctors, especially in the U.S. Looks like we are on our way though with the University of Chicago planning on a clinical trial in UC patients with fecal transplants possibly as early as this fall.http://www.sciencedaily.com/releases/2011/06/110602091838.htm

I’ve attempted the fecal transplant both rectally through a fleet enema and orally by basically drinking a shit-shake. I’m currently writing about my experiences on my blog. The short story for me is that it worked, but only for a day. I have constipation, trapped gas, and bloating symptoms that were alleviated after the oral ingestion (which was quite nasty, by the way). I think the efficacy of this procedure depends a lot on selecting a proper donor.

In the future I hope to find a donor in a younger person who was raised on a Weston Price diet (of which there are many kids these days) or maybe a Sudanese refugee or someone along those lines who might have optimal bowel flora.

Checking in again. It’s been two weeks now since my original fecal transplant. It’s been kind of a bumpy road. The first 5 days after the original infusion, things were good, I had a normal amount of bowel movements a day. Then I jumped back up to about 6 a day. I did another fecal enema last weekend, and since then, things have been stabilizing again, about 3-4 a day and mostly no nocturnal bowel movements, that’s good for me!

I have been wondering a few thing about fecal transplants and Crohn’s. Dr. Borody in Australia, who is basically the pioneer for doing fecal transplants on IBD patients mainly focuses on Ulcerative Colitis patients (besides c. diff) and not Crohn’s. I used to think it was because Crohn’s can affect the whole digestive tract and not the colon. However, I just listened to an interview with him, and he suspects that since Ulcerative Colitis attacks the whole colon, it seems to show it would be a reaction to gut bacteria, however since Crohn’s is patchy areas of inflammation dispersed between healthy tissue, he thinks it is more representative of an infection and not a reaction to the gut flora. He proposes that a lot, but not all, Crohn’s cases are related to MAP http://www.ncbi.nlm.nih.gov/pubmed/11926571.

I originally thought that since my Crohn’s responds very well to antibiotics that the opposite, a human probiotic, would be the answer. Now I wonder if the fecal transplant will be enough.

Can MAP respond to dietary measures alone as in following the PHD? I’m hopeful that this fecal transplant will help, but I’m wondering if it will be enough. I’d hate to go on antibiotics again and undo everything I just did, but if I flare again, I wonder if it’s because my Crohn’s is an infection. When I get really bad, I’ll get high fevers up to 103, which is not that common for Crohn’s patients, and it seems to be more indicative of my body battling some sort of infectious agent. Dr. Borody mentions using the antibiotics for years, and I wonder the pros and cons for that, if it will permanently alter your gut bacteria, but then again Crohn’s is horrible in itself.

Just wondering your thoughts on if Crohn’s is indeed an infection, do you think fecal transplants and dietary measures would be enough to stop the disease, or is it most likely I’ll need to get on a long course of antibiotics?

I like Dr. Borody, and I think he is on the right track. I’ve always thought Crohn’s was more likely to be infectious than autoimmune.

Are you doing antibiotics along with the fecal transplant?

The small intestine is a relatively antiseptic, low flora site, and so fecal transplants aren’t as effective at displacing pathogens there. So the chances are much better with ulcerative colitis than Crohn’s. Still, we don’t know if it will work until it’s tried.

I think probably antibiotics, antimicrobial plant foods, replacement probiotics, and lots of sunshine are probably the best therapies. Fermented vegetables and oral supplements may be sufficient for the small intestine. I’ve found that Chinese herbal medicines work well against fungal infections and might be helpful against some bacterial infections in the gut too. Most traditional spices are antimicrobial so eating spice-laden food including green spices and turmeric are good bets.

Chronic infections tend to take a long time to cure. How much of that is because of bad diet, and how much is intrinsic to these diseases, we can’t know yet. If you do everything right I wouldn’t be surprised if you can cure it in months.

I was under the impression that taking antibiotics while doing fecal transplants would be counter productive. Wouldn’t the antibiotics kill all the bacteria from the infusions? I am not currently taking antibiotics, though I did take them before I did my initial transfusion via colonoscopy.

I am getting some fermented veggies, eating kefir & yogurt as well as some s. boulardii, so I’m trying to keep up the beneficial bacteria.

My Crohn’s hasn’t affected my small intestine yet, so I’m hoping the fecal transplant will work. My disease is in my colon, however my gums (and sometimes mouth get inflamed when I flare, so I’m not sure how that affects things.

I will say that I have definitely seen an improvement since I got my first infusion. Perhaps this won’t be the whole cure for me, but I think and am hoping it is a large part of it.

Yeah, I kind of figured that my small intestine might be involved, but all the tests they’ve done so far have not confirmed that. I suppose the worst part involves my colon. In any case, like you said, you don’t know until you try. And yes, improvement is definitely a good thing.

I hope you don’t mind that I keep coming back here for advice from you. I appreciate your outlook and advice.

I’m almost a month out from my original fecal transplant for Crohn’s. I was doing fairly well, had some bumps in the road, but was stable and better than before the transplant.

Last weekend I seemed to take a nosedive, and symptoms are returning. Two things that may have impact are that:

1. I had been doing home infusions but wasn’t able to do one last weekend.

2. I did run for a bit (used to be a pretty serious runner before Crohn’s), which I hadn’t done in a long time, and I pushed the pace but not the distance.

Along the lines of thinking that my Crohn’s is possibly an infection, I have a few questions on the best route of healing.

• I meet with my GI next week to discuss options on treatment. I could ask for Low Dose Naltrexone, which seems to help others, but I’m wondering it’s effectiveness if my Crohn’s is infective. I also exercise regularly, so if it’s endorphin related, I’m wondering if I would really be deficient. Any thoughts on LDN? I know you mentioned in the past you were still deciding.

• I could also try an immunosuppressant, but I doubt it will work since I’ve tried others before (as well as biologics which only worked a few months). Or I could ask about the anti-MAP protocol which combines 3 antibiotics for the long term. I’d hate to undo all the work I’ve done with the transplants, but I’m wondering if that’s the route to go. I’ve responded well to antibiotics before, but I’m a little fearful of being on them long-term. Any suggestions on which may be the best course? Any thoughts on the use of long-term antibiotics?

• As far as exercise goes, I have cut way back since I got sick, but I wonder do I need to really be cognizant about resting if Crohn’s is perhaps an infection? I do rest a lot more, but after running, I noticed a jump in symptoms, perhaps from pushing my body too hard. Any thoughts on exercise when you’re trying to recover from a chronic disease?

Re LDN, I need to do some research on it. In general, the immune system’s default state is a balanced one which is optimized for a wide range of infections — good but not great at each one. When you modulate immunity, it becomes better at some infections but worse at others. LDN is probably like that, helping against some but not others. I haven’t researched it enough to judge which infections it will help against and which it won’t. Also, we don’t know your pathogen (true?), so even if we knew what LDN was good against, we wouldn’t know if it would help you.

You could consider an experiment with LDN to judge whether it helps or hurts.

Also, if you haven’t already done a DNA stool profile like the Metametrix GI Effects Profile, I would ask to have that done.

I would avoid immunosuppressants. Do LDN first.

I do think you should listen to your body. Rest can be very important in infections, and usually your body will tell you if it needs rest.

Personally, I’ve been resting for years because of my infections, and am only now getting gingerly back into exercise. If you do exercise, I would go for intensity over distance. Tabata protocols might be the best cardiovascular workout. But rest might be even better.

I’ve been following your discussion with interest. I have either Crohn’s or some kind of bacterial overgrowth in my small intestine (still not sure, though the results of a capsule endoscopy (due in a week) may shed some light). it’s been around for about 2 years, and came on suddenly (I can pinpoint it to the day), possibly due to drinking untreated well water, but I guess I’ll never know now.

At the start, the only thing that made a dent in my symptoms (gas, gurgling, fatigue, feeling spacy as hell) was grapefruit seed extract capsules, which worked REALLY well. Have been on a low-carb SCD/Paleo diet (with some dairy – mostly organic high-fat yogurt, some butter – not much milk) and religiously taking digestive enzymes & betaine HCl with every meal for the last year, and that’s worked quite well (almost no symptoms aside from the odd 1-2 day flareup of gurgling/belching every few months when I fell off the wagon and ate more carbs than I should’ve), although I’ve had a quite bad flare-up recently (3 weeks (!) of belching after food, cramps, some nausea, and extreme fatigue) that’s made me decide to get it sorted for good.

How do I get my hands on those Interfase enzymes from Klaire labs? Their website says they distribute only to doctors (and I’m not quite through medical school yet). Also, I’m in the EU…which may complicate things. If only they sold it on iHerb!

Thanks for your input. This may be a stupid question, but this is where I get confused with conventional medicine thinking vs. “alternative”. I was under the assumption that I wouldn’t be able to find out what causes my Crohn’s, since there supposedly is no cure. If I get the stool testing, will that tell me the exact pathogen that is causing my Crohn’s? You are correct in that I’ve not had the test done yet. I was hoping the fecal transplant would take care of things. I hope my GI will be on board with ordering the test for me. I believe when I checked, you have to have a doctor ask for a kit.

Yeah, I’d rather not be on an immunosuppressant. LDN at least seems a lot less harmful than the other options.

One more topic I forgot to ask regarding Crohn’s. I’m still getting through your book. You mention that certain diseases/infections are best handled under a ketogenic diet and others are actually worsened by too low of carbs. Do you think Crohn’s is probably a disease that would respond well to ketosis? If yes, do have any experience with why ketosis causes insomnia and how to get over that? I tried a ketogenic diet in the past and found I had a horrible insomnia, when I sleep well otherwise.

Sorry to hear you have this horrible disease, though I certainly feel less selfish now in asking Paul my millions of questions. At least it may be helping others.

I got the Klaire lab enzymes from Amazon.com. I’m not sure, but there may be a link on this site that you can buy them through and hopefully support the Jaminet’s website.

I’m on SCD too. Do you mind my asking how low of carb you had to go in order to see progress and when you started to notice progress?

I’d be interested to hear what your GI docs say about fecal transplants. It doesn’t seem to be well accepted in mainstream medicine yet, even for c. diff it seems to be a last resort. I hope that changes, because I do think it has great potential.

No, there’s no guarantee the stool test would tell you what is causing your Crohn’s. First, the small intestinal pathogen could be different from the colonic flora that appear in the stool. Second, they test for the 40 or so most common pathogens, but you could have an uncommon pathogen.

However, if you find high levels of a pathogen in the colon, there’s a good chance it may be causing problems elsewhere. It gives you something to treat and then you can see what improves and what doesn’t.

Ketosis could cause insomnia for two reasons: either because it’s helping or hurting. If it’s helping you kill your pathogens, it will cause die-off of pathogens, and increase circulating pathogen die-off toxins that are known causes of insomnia. The cure for that is to take something like cholestyramine (or bentonite clay, or charcoal) to help excrete the toxins. If hurting, it means you have a fungal or protozoal infection that is benefiting from ketosis, or you are entering ketosis with excessive restriction of carbs and protein (you should get into ketosis with short-chain fatty acids, while still eating carbs and protein).

I definitely recommend trying cholestyramine. That might be your next step with your doctor. It can significantly relieve symptoms from lipopolysaccharides and other toxins. Reducing the toxin effects may clarify symptoms and help you diagnose the pathogen.

To say you are a wealth of knowledge is an understatement. I see what you are saying, basically I have to peel back the layers to figure out the root cause or causes of the disease. I was hoping it would be as easy as a poop, but apparently in my case, it’s not. 😉

I (obviously) never knew that about ketosis-induced insomnia. Very interesting about how die off pathogens cause insomnia. When I did try a ketogenic diet in the past, it was due to severe restriction of carbs, so I will know now to not to restrict so much.

Paul – cheers for the link. I’ll be trying that out when my next pay cheque comes through. Also, thanks for all the info so far – highly informative.

CG – I wasn’t in the middle of a flare when I started, so YMMV, but I started the SCD and the enzymes/acid (which were CRUCIAL) at the same time – I guess it took a few weeks for me to feel really better, but the gurgling and stuff stopped almost instantly, within days I would say.

I’ve discussed various therapies with GI docs, both as a patient and as a med student – many are frustratingly, almost amazingly unwilling to consider alternatives to the standards, but that kind of investigative treatment is much more expensive and harder to justify on the NHS, where clinical guidelines are king. It’s one way that private medical care exceeds public care (if you have the insurance/cash, of course!).

Generally, though, if your consultant (I think you call them “attendings” in the US, though I’m not 100% sure) is based out of a teaching hospital, and you can back up the rationale for your desired treatment approach with some preliminary (scientiic) evidence, and you hint at the possibility of getting a journal article published, they’ll be a lot more receptive to the idea. 😉

Any opinion on oxygen-based colon cleaning? Combined with probiotic enemas afterward, wouldn’t that be similar to a fecal transplant? Trying to address a perceived dysbiosis/candida problem.

I experimented with hydrogen peroxide enemas this past Christmas and got an unbelievable amount of white stringy stuff out over the next 2 months which I believe to be Candida – the fungal form (~50 feet total).

H202 enemas were apparently popular in the early part of the 20th century for removing fecal impactions, but aren’t in use much any more. Not a lot of information online.

I’ve been taking probiotics for 10 years and suspected they were not taking root. Have been taking “soil” bacteria products like Primal Defense, Nature’s Biotics, & Flora Balance since the early 2000’s without any real success. The gut profile and biofilm information is very enlightening.

Am taking sacchromyces boulardii right now which definitely seems to help.

I have had some Gl issues since grade 11. I was given antibiotics for my wisdom tooth and since after that i have had some gl issues which were diarrhea once per month. It wasnt that bad but after exactly a year after i was given the same anitibiotics again for a cold virus. But this time i ended up getting a lot of Gl issues; lactose, gluten and soy intolerance. Anyways, i wanted to know if i was able to do the fecal transplant at home.

I wouldn’t start with a fecal transplant, I’d start with fermented vegetables. Learn how to make sauerkraut-style fermented mixed vegetables at home; drink the fluid they ferment in and eat the vegetables.

Firstly, thank you for replying. It means a lot. Now the thing is, the reason why i was saying for me to do a fecal transplant its in order to replenish my gut with the bacterias. Because after the antibiotics, from what i have learned,the bacterias in the gut are altered forever. And since i have lost a good portion of my bacterias, i have gained food in-tolerances. Even thought, im slowly starting to gain my back my tolerances to certain foods that i have had lost after my antibiotic treatment, i want my gut to be replenished in order for my digestive tract to work at its full potential just as how it use to. I didn’t mention everything in the earlier post. In grade 9 i had taken antibiotics for 6 months for acne which had caused me to have diarrhea for almost a year but back then i never really cared. Basically, each time i have taken antibiotics, it has aggravated my situation and now this time, it has deeply affected me. And also, i have also learned that sometimes the antibiotics could almost bring the gut population of the bacterias to almost zero. I have tried one of the best probiotics in the market, it hasn’t done anything. I went to go see my G.I Specialist, and everything in my intestines seems to be fine, no parasites, c diff, ulcers or any ibd.And he doesn’t know what is causing the sharp lower stomach pain, weird looking stools, food in-tolerances and my occasional diarrhea. SO my conclusion is that my bacteria in my gut has been altered and therefore my symptoms have gotten worse. Now how are these fermented mixed vegetables suppose to revive differents species in my gut? I am going to speak to my G.I about this, and as it says in this article that the fecal transplant are the best probiotics.

Since my daughter is a type O and coconut is not recommended for her blood type. She gets nausea and upset stomach when she eats coconut, also concerned with putting on weight when eating too much fat. Do you have any other suggestions for increasing ketosis, food sources, or just go with leucine and lysine to help stimulate ketosis? I believe that she has a fungal issue as she has a wheeze in her lungs from time to time, so maybe she should not to ketogenic diet or ketogenic fasting and stick with PHD, and just incorporate other healthy fat such as salmon and sardines (which you recommended). Thank you Paul.

I would try MCT oil first. You can find that on Amazon via our recommended supplements page. It is usually tolerated much better than coconut oil.

I would go with leucine not lysine if she wants to try the amino acid route. But MCT oil is the safest and most effective route.

If she does have a fungal infection than a ketogenic diet is not advisable. If she’s not sure, then if it gets worse on a ketogenic diet that would be evidence in support of a fungal diagnosis. Is there other evidence of a fungal infection?

Thank you so much for your reply. Other signs of fungal infection would be a white tongue and a soft spot on the crown of her head(not sure that is necessarily related), asthma, gut issues (bloating, weight retention during the time of month). She recently lost 20 lbs doing the HCG diet but we have not healed her gut yet. She has been taking probiotics, enzymes, fermented veg. (not enough but adding slowly), started drinking broth in the a.m. and is generally a healthy eater. She is in college and puts alot of stress on herself (biochemistry major) and causes alot of these issues starting in highschool. Thank you Paul.

I was diagnosed with a gastritis and an inflammation of the large bowel about 2 months ago .
Now i got the diagnosis that i have an intolerance towards histamine and lactose. Also Gilbert syndrome was diagnosed.
I might be a little desperate right now because to be honest, i have no idea how my diet should look right now. It is like everything is giving me either diarrhea, bloating or heartburn. Even if im eating just rice with vegetables, olive oil and chicken it is still the same. Im taking the supplements you recommended and overall im a pretty fit guy, just my digestive problems a really confusing me.
Im sure you are very busy, but maybe you can help me create something like a proper diet.

Subscribe

Come to the Perfect Health Retreat

Come join us for a week at the beach learning how to achieve a lifetime of great health!

Buy our book

Perfect Health Diet: Regain Health and Lose Weight by Eating the Way You Were Meant to Eat is a great way to understand the dietary and nutritional practices that lead to optimal health. Click the image below to visit our "Buy the Book" page: